THE FIX
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If you think Windows starts up slowly enough as it is, you can disable WGA by removing the execute bit on WgaLogon.dll. That way, winlogon can't call it as a notification package at boot, and since WgaLogon is responsible for running and maintaining WgaTray.exe, no more tray popups either.

And since the read bit is still there, you won't trip Windows Update to force you to reinstall it; the DLL still matches with the WU catalog and all the WGA registry keys are still in place.

HOWTO
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If you're not familiar with how NT ACLs work, here's how you can break file permission inheritance. First of all, let's make sure Windows will let you access the ACL dialog from the GUI:

I often have to reinstall operating systems on machines because they get screwed up either by some spyware, a virus, a program that had too much fun during an install, windows just crapping out, drive dying, etc.

This is something that I have to do quite often for many other people. Up until this point, I would install the Corp VLK release just so I didn't have to deal with activation.

I had a situation like that just the other day. A dell laptop that had a legit sticker of XP Pro came in to buy another version of XP Pro because Microsoft said his copy wasn't legit. Microsoft is stepping beyond their rights now, I fully support a cracked copy in those situations that people PAID for their product and now, because of DRM, doesn't work.

2014 is going to be a good year. More content, more streamlining. Be a part of history!

you mean NT supports UNIX-style (or close) file permissions and hides them by default ??
I mean, this means NT has built-in support for the most basic form of UNIX security, but uses win95-style (==absent) security by default.
/me backs off in disgust

they are hidden from the mortal user at least
I only ever knew of the ro, hidden and archive bits. (if there are other bits like that, them as well). There were the bits Total Commander displayed, and they never bothered me in the slightest, i.e. I never had problems finding hidden files and similiar.